Squamous cell lung cancer (SQLC) is the second most common lung cancer subtype after adenocarcinoma and accounts for 30% of all lung cancer cases. However, in contrast to adenocarcinoma, SQLC lacks therapeutic targets like activating EGFR mutations, ALK or ROS translocations. Besides immune-checkpoint-inhibition a promising treatment option in SQLC is the recurrent amplification of the tyrosine kinase fibroblast growth factor receptor 1 (FGFR1) within the 8p12-p11 region. Thus, small molecules inhibiting FGFRs have been employed to treat FGFR1-amplified SQLC. However, only about 10% of such FGFR1-amplified tumors respond to single agent inhibitor therapy. To investigate the mechanism of FGFR inhibitor resistance in 8p12-p11 amplified SQLC we performed deep genomic and transcriptome sequencing on 53 FGFR1 amplified samples including primary tumors (n=33), patient derived xenografts (n=13) and cell lines (n=7). For 22 of these samples the response to FGFR inhibition was known. We detected frequent breaks within NSD3 (n=3), also known as WHSC1L1, favoring the expression of NSD3-short, which is known to enhance MYC expression. Furthermore, the amplification pattern for all samples was compatible with a breakage-fusion-bridge (BFB) mechanism, showing chromosomal telomeric losses, copy number, and frequent intrachromosomal head to head and tail to tail breaks. Genomic reconstruction of one sample suggests a tandem duplication followed by a BFB mechanism, implying that the BFB mechanism is a later event in tumor genesis. Intrachromosomal tail to tail fusions within a 400kb region close to the FGFR1 open reading frame, have been detected in 75% of patients with a partial response to FGFR inhibitor therapy (3 of 4 patients). A similar break was detected in the FGFR inhibitor sensitive cell line H1581. All samples, which responded to FGFR inhibition (n=9), demonstrated a centered amplification pattern on NSD3 / FGFR1 and excluded amplification of the adjacent disintigrin and metalloproteinase family members (ADAM) genes. In contrast, the main amplification peak of the non-responding samples (n = 13) was centered on ADAM family members, corresponding to an increase in ADAM expression. These data suggest strong relevance of these genes for tumor development and growth, and warrant further investigation.

Citation Format: Florian Malchers, Martijn Henricus van Attekum, Martin Peifer, Roman Kurt Thomas. 8p12 amplification pattern dictates FGFR1 dependency in squamous cell lung cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 412.